Twilight's Prime
by Phantom Fan 21
Summary: Strange space Ponies form space appear and been attack Equestria for three weeks. Twilight Sparkle and three fighters has team up to stop them. But why is Twilight magic blue after the fight? "GOING TO REWRITE IT!"
1. Chapter 1

**Twilight Prime**

**A crossover/fusion of Metroid and MLP.**

**Phantom Fan 21: **Here a second game crossover for one of the Mane 6. Now unlike Twilight "Metal Gear Sparkle" Stories, this will not be in game order. This will be like Metroid Prime 3 only mix with the order Metroid games. Twilight won't met Samus but will get her weapons and upgrades. To her they will be spells. They are the Morph Ball, Bombs, Charge Beam, Ice Beam, Wave Beam, Plasma Beam, Varia Suit, Gravity Suit, (Which just make a orange and dark purple glow around her), Speed Booster, Missiles, Super Missiles, (Which will be two powerful blasts from Twilight horn, one red and the other green) Power Bombs, and the Screw Attack. I think I got the all the first weapons from the first Metroid game. I know the Speed Booster, Super Missiles and the Power Bombs are not in it so I went with the remake. Now also like Metroid Prime 3 Twilight get affected by Phazon and has control over it, however she learns it slowly takes over her. She call the Phazon in her Prime, because it use just like her magic. I even thought of the corrupted looks for Twilight when she goes in a over load. At 25% her eyes has a faint blue to them, At 50% Twilight fur coat becomes a blue-purple color showing the corrupted has been growing and At 75%, Twilight eyes are show to be fully blue and her fur coat grains a dark purple color much dark then her normal fur coat color. Feel free to draw them, due it I can't draw and put up pictures because I don't have a scanner.

Now that out of the way, I not going to use the same Space Pirates from the game, but I will use a new type of pony that come from space that want to destroy all of Equestria. They will be call Space Ponies Pirates. Now the first chapter will look rush but I say this now, The Space Ponies Pirates arrived and be attacking Equestria for weeks started with Canerlot since they, the Space Ponies Pirates, think it the powerful place on the plant. They fight as be going on for three weeks and ether side has grain or loss anything. Now Princess Celestia has a plan that will defeat the Space Ponies Pirates and make them leave, will it work? Also keep eye out on what Twilight will look like when she using the Phazon even when corrupted. Also two charters form the show will be use to be Kraid and Ridely, namely one will be a Changeling and the other will be a Dragon. I don't think there a creature that fit Kraid. So I using a Changeling. As for Ridely, will of course I'm going to use a dragon after all Ridely look like a dragon. Will let get on with the story. Here how Twilight get Phazon in her and met the Space Ponies Pirates and their leader.

* * *

_'It been three weeks since these Space Ponies attack our home. We been fight back strongly but ether side has grain or lost ground. Now I been send to help my brother, Captain Shining Armor, to deal with the Space Ponies. Celestia believes that my smarts will help stop the Space Ponies attack. I just arrived at Canerlot and it steams empty without anypony around. Still I have to help any way I can. I just hope I can stop the Space Ponies before we lose Canerlot-Twilight Sparkle at 0230 hours'._

Twilight step in the castle and two guards greet her. "Hello Twilight Sparkle, Because of the of the new space invaders Celestia has a new security that all doors can only be open by a unicorn blast from it horn. We know you are already skill unicorn, try hitting all the targets around the door." The Guard said.

Twilight look around the door and saw four red targets. Her horn glow a purple glow and she fire at each target. Soon all four was turn green and the doors open.

"Well done, The Princess made the right choice as you to be her student." The guard said and Twilight walk thought the doors.

_'Yes, I'm Princess Celestia Student. After entering a school in the castle I was given a test, to hatch a egg. I couldn't do it no matter what. Just as I was giving up hope, a loud sound, which I latter discover was the Sonic RainBoom, made my magic grow stronger and hatch the Egg. That when I met Spike. He still a baby Dragon but I love him very much and he like a little brother to me. Sadly after the test was done I lose control of my magic. I not sure what I did, but I did know that Celestia hoof appear on my shoulder and my Magic stop and undid the spells I did.- Twilight Sparkle.'_

Twilight walk through the castle and so reach other guard.

"Ah, Twilight! Celestia wanted to remind you that high spells are not to be use unless we are attack but we know you are still learning, so I have a spell that might help. See those targets over there?" He said and pointed at them.

Twilight turn and saws them.

"This spell is really powerful but I think it best you know this incase you do need it." He said and an Red glow appear on her horn and fire at one of the targets. After that he breath hard before looking at her.

"This spell is call the Red Blast spell. It really powerful and only should use if need. With practice you can use it to help you." He said.

Twilight nods and the guard moves out of the way and Twilight step in the throne room where Princess Celestia along with the Griffon King, Dragon Lord, and a Diamond Dog leader stood with her. Each had a guest with them.

"Well, well, if it isn't Rainbow unicorn friend." Said a voice Twilight knew well.

"Gilda! That enough." The Griffon King said.

"You! Your that pony the friends with the whining unicorn." Said the smaller Diamond Dog.

"I'm greatly sorry for what my soldiers did to your kind Celestia." The Leader said.

"It fine, Twilight. It time to talk about a plan." Celestia said before turning to Twilight.

"Yes Princess." Twilight said and walk next to her.

"Now that everypony is here, it time to start. As you all know we have been attack by Space Ponies." Celestia said.

"Yes, they are powerful but doesn't steams to gain anything from the fight you been having." Gilda spoke up.

"Gilda! That maybe true but what to stop them from coming to our homes as well?" The Griffon King said.

"True! We may not like each other that much, but we share a common emery. We have to work together to save our land." The Dragon Lord agree.

"By the way Miss Twilight.", A dragon said turn to her, "How do you know the Princess?"

"I'm her Student." Twilight answer.

"What?! That not possible!" Gilda shouted.

"It true, but we are getting off track.", Celestia said, "The Space Ponies had try to storm the castle, but fail and retreated."

"We now know that they hide in the fields wanting for their next move to plan out." Dragon Lord spoke up.

"The only way we can stop them if we send some kind of team that will stop them while they are unready." The Leader said.

"I don't think that will work, but I do have a plan." Celestia said.

Twilight turn to Celestia, she already knew she had to help her brother in the battlefields and waited until she heard the Princess's plan.

"We will send our best fighters to my army to help the fight, if the Space Ponies see that races are working together they might get scare and flee, hopefully." She said.

"Well Gilda, you better put up a good fight and be nice to the others." Griffon King said looking at her.

"Yes Sir." Gilda said growling.

"Smoke, are you ready for the field of battle?" Dragon Lord ask the smaller black dragon.

"You got Sir! They won't know what hit them." Smoke said blowing smoke from his nose.

"Digger! I better see good results in your fight or you will go back to digging." The Leader said.

"Just let me at them! These teeth and craw will tear them apart!" Digger said baring his teeth and craws.

"What about you, Twilight?" Smoke ask.

"I'm been send to help my brother." Twilight said.

"Really? Wow! Your brother out on the battlefield? I would like to met him." Smoke said surprise.

Then the castle shook and the guard came running in with Luna in front of them.

"Sister! The Space Ponies are attack the castle!" She said.

"What?", Celestia said surprise, "We must fight back, all four of you do what you can to save the castle."

The four fighters (though Twilight dislike fighting) ran out and saw the Space Ponies attack the guards. Twilight was quick to spot one head for them and send a magic blast that knock it away.

"We better spit up. If we can take them down then we have a chance to save this castle." Smoke said.

"Right! Let's give them a good fight." Digger said.

"Twilight, I know you not much of a fighter, but I know you can do anything to save the castle." Smoke said and the group ran off.

Twilight turn back to the Princess and she nods. Twilight runs in to the fight unknowing her life will charge forever.

* * *

Twilight ran though a hall using her magic to knock all Space Ponies away from her. She duck under one Space Pony and use a spin kick to knock it out.

_'I not really a fighter, but my friend Rarity has teach me some hoof to hoof combat the will come in handy for times like these. Still this Space Ponies are strange. They just attack us as if they were waited for us to be here. Ether way they have to be stop. There only one thing I know they will try to good for. I just hope they didn't getting there yet.-Twilight.'_

Twilight ran thought castle and was jump by one of the Space Ponies. Before it could attack Twilight smoke cover the area and a sound of swift movement was heard. The Space Pony felt pain over it body as someone or thing attack it.

Finally the smoke clear and there stood Smoke standing over the Space Pony.

"They maybe sneaky but I'm sneaker." He said before turning to Twilight.

"They steam to be heading towards the lower part of the castle. I was just on my way to tell the others when I saw you. Thought I give you a heads up and now you own me one." Smoke said.

"Thanks, I met you and the others there. I know my way around this place." Twilight said and Smoke nods and fly's off.

Twilight then head back down the hall taking out more Space Ponies. Unknowing two reptile like eyes was watching her.

* * *

Twilight runs until she a guard throw toward her. She caught him with her magic and set him down.

"Be careful, that thing is stronger then it looks and has some strange magic." He said before fainting.

Twilight look and saw a giant Space Pony walking on it back hooves and roar as it near Twilight.

Twilight ready her horn and the Giant Space Pony charge at her. Twilight jump away and fire a spell at it, but the armor it had was tougher then the ones she fought before.

Twilight jump out of the way of it giant hoof and continue to as it try to stomp here again and again. Finally they back out to a large balcony and Twilight saw she was going to have to fight it.

"I maybe not like to fight, but something tells me you not going down without one." She said and a red glow appear on her horn.

The creature reason with glowing spots of it own. Twilight aim at one of them and fire. The Red Blast did the trick, the glow spot blew up and the creature roar in pain. Twilight build up another Red Blast and fire at the second spot. It too blew up and Twilight could see it weak spot on it head.

The creature roar and charge at Twilight, who jumps out of the way and then runs up to it back and jumps on. The Creature try to shake Twilight off, but she had a good grip on the shoulder plates of the armor. She lift her head over the weak stop and said, "Don't mess with our Kind! You never know what could happen!" and fire a Red Blast at point blank range.

The Creature roar as Twilight jumps off it back and lands on all four hooves. The Creature try's to stay on it hooves back too close to the edge and fell over into miss and disappear. Twilight look over the balcony to see no signs of it.

_'I had no clue on what it was but I need to get to the city. The Princesses have a secret bunker there. In there is the Elements of Harmony. I just hope the Space Ponies didn't get there first.-Twilight'_

* * *

Twilight met up with the others as she step out of castle.

"What took ya? We were going to leave you behind." Gilda said.

"They are after something. I can tell." Digger said.

"Hey relax guys, we stop them right Twilight?" Smoke said then ask Twilight.

"I hope so. I know what the are after and I hope we are not too late." Twilight said.

Twilight lean them thought the city and to the bunker. Twilight started to use her magic to open the door when something come zooming from the sky.

"Heads up! Something coming!" Gilda said and they all get ready to fight.

A creature land and fire a blue beam at Digger who charge at it and was knock back. Gilda was able to get close and threw a few attacks, but it dodge them all. Then punch her away. Smoke threw some fire balls at it hoping long range will work better then short. But the Creature put up an blue shield to block the attack and send a blast back at him. Then turn to Twilight and fire another shot. Twilight move her head to the side and the attack miss. Then she fire her own shots back at it. Twilight was able to score a few hits and knock the creature back. The other stood up and ready themselves to attack. Then the creature stood and started to glow blue around it body. Then release a powerful beam that knock all of them off there feet.

The Creature walk over the falling fighters and stop at Twilight. It lift her with a blue glow. Twilight open her eyes to see the creature was a mix of her and a Changeling. It lean to her ear and spoke in a voice that was a mix of her and Chrysalis, "Thank you for freeing me." And drop Twilight. Twilight watch as it walk away, not even taking the Elements of Harmony. It flew away as Twilight black out.

* * *

Back at the Castle, Princess Celestia and the leaders of the land watch as the Space Ponies retreated like their leader was defeat.

"They retreat, that odd." The Dragon Lord said.

"Yes, that is odd. I just hope they didn't get what they were after." Celestia agree.

Then a guard come running in.

"Princess! Good News and Bad News. Good news is the Space Ponies are retreat as you can see." he said.

"Did they find them?" Celestia ask.

"No the Elements are still in the bunker." He said.

"That good." The Diamond Dog Packer Leader said.

"The Bad news is we fond Twilight and the other knock out as if some pony blast them in one shot. They are being brought to the hospital as we speak." he said.

"They must have fought the leader and might have been to powerful for them." The Griffin King said.

"We will take our own fighters back to our lands." The Dragon Lord said.

"Yes, but remember they may return. For now, I must see my student." Celestia said and walk away.

* * *

I know, it not like the start of Metroid Prime 3, but I what to get this done. Up next Twilight learns about Phazon and the powers she gets. The Phazon will give her the Morph Ball, Bombs, and Charge Beam. Morph Ball as you can guess turns Twilight into a ball that fit in tight places. Bombs are just small energy spells that Twilight lay around. And the Charge Beam act just like the games. Send me some tips on who be the first boss. And Riley is being save for later for he out. There is a Dragon playing him but it not the two Dragons you read here. Please review.


	2. Chapter 2

**Twilight Prime**

**A crossover/fusion of Metroid and MLP.**

Doctor Stable was looking over the X-rays of Twilight's body. She didn't have any broke bones but he wanted to make sure. He put the X-Rays down and pick up some pictures that show Twilight's insides. Everything look fine but something was odd. Whatever happen to Twilight it was rising questions.

Twilight has been a sleep for a long time and sometimes her body gave off an blue glow. What was it? Where did it come from? Why does everything look fine on Twilight when it clear she was in a tough fight? Those and more rise in his head. He look at a picture of Twilight heart for the fifth time. Now that he was looking closer unlike the last four times he look at it, He notices there was something there.

"What is that?" He said and took the picture and walk to take to his staff. He need to get better view before he report to the Princess.

* * *

A short time later, Princess Celestia and Luna, Twilight friends and her family was standing with Doctor Stable who was going over the notes one last time.

"You what to see us?" Shining Armor ask.

Doctor Stable look up and said, "Yes there some thing I what to show you all, but I really wanted to show just the Princesses."

"Hey! Twilight our friend. We are worry about her too, You know!" Rainbow Dash said.

"And Twilight family has been worry sick once they heard about what happen." Rarity added.

"Very well, look at this and tell me what you see." Doctor Stable said and put up a picture.

"Dud! It Twilight's heart." Rainbow answer not knowing where this was going.

Doctor Stable switch the picture with a bigger and ask, "How about now?"

They look closer and Candace said, "I see something on her heart but what is it?"

"That we don't know. We thought we might try to remove it..." Doctor Stable started to said before Rainbow Dash cut him off.

Then way don't you? Who knows what it doing to Twilight." She ask.

"We can't! We don't know if Twilight will live if we take out her heart and place it back in after we remove whatever the thing is. There a 5% chance she will live!" Doctor Stable stated that they thought about it, but knew the risks was to great to try.

They other look down at this news.

"So it going to stay on Twilight's heart?" Fluttershy ask.

"Yes, I'm afraid so." Doctor Stable said.

Then Nurse Redheart bust in.

"Doctor Stable! Twilight Sparkle is awake!" She said.

* * *

Twilight open her eyes to see that she in the Ponyville Hospital. She stood up and look around. Then grab her head. It felt somepony stomp on her over 100 times and didn't crack her horn. She heard the door open and Nurse Redheart step in looking at a clipboard.

Twilight stood up some more using her hooves to keep herself up. Nurse Redheart look up from the clipboard to see Twilight awake. She gasp and ran out of the room. Twilight got out of the bed and fond she felt better then in her own life. She being to bend her body as if the be stuck in the same position for a really long time. Then a strange thought appear in her mind.

_'Morph Ball Ability activated! Can now fit in tight places. To use, roll yourself into a ball and spin to move.'_

Twilight was a little surprise to hear a thought. She then thought about try it to see if it work. Twilight bend her head down to her legs and grab them. Her mane and tail steams to cover her whole body. So she look just like a ball. Her Cutie Mark was show in the middle of the ball form. Twilight being to spin herself and started to roll all over the place.

_'This strange ability make me into a ball and said I can fit into tight places. But where did it come from? And why does it feel like my body is better then in my life? But one question stood out from the rest. The Changeling that look like me. What did she mean I 'free' her? Who was she?-Twilight Sparkle.'_

Twilight roll around some more and then went under her bed just as the door open and everypony she knew came in and saw the empty room.

"Hey! Were did Twilight go?" Rainbow ask surprise to see a empty room.

"That odd, The door was shut and the windows aren't open, even if magic was use we would have know." Doctor Stable said in the same type of confusion.

The a purple mane like ball roll from under the bed and stop a Fluttershy hoof.

"Nice Ball Fluttershy!" Pinkie said pointing to it.

Everypony look down and Fluttershy said, "It's not mine."

"There were did it come from?" Shining ask.

The ball move away from Fluttershy and stop at the bed. Then they watch as the ball uncurl back into Twilight.

"Well it is odd, but something tell me it can be useful for some things." Twilight said before she was jump by all her friends.

"Glad to see you awake at last Twilight." Rainbow said first.

"Ya had everypony worry then a needle in a hay stack." Apple Jack said next.

"We thought we might lose you, but you're still here." Fluttershy said happily.

"I throw a "Glad your awake" party! After we leave of course." Pinkie said then added before Nurse Redheart could tell her other wise.

"So Darling, how did you turn into a ball? Is it some kind of new spell?" Rarity ask.

"Well, actually it kind of strange. I heard this thought in my head saying that I can use what call the Morph Ball to fit in tight places." Twilight answer.

As soon as Twilight finish said that an new thought enter her mind.

_'Bomb ability Activated! Can now place small energy on the ground and blow up cracks. To use, go to Morph Ball and place them on the ground, they will make you jump if you are over them.' _

"Hey Twi! Are you with us?" Apple Jack said snapping her out of the thought.

"Yeah, just another strange thought has enter my mind. Telling me that I can use 'Bombs' when in my Morph ball mode." Twilight said.

"BOMBS?!" Everypony expect the Princesses shouted.

"I was told that it just a small energy that blow up cracks, But something tells they might get stronger." Twilight said thinking about it.

"Well it might because of the thing on your heart." Doctor Stable said.

"My heart?" Twilight ask.

"Yes, a strange thing, I don't know what it is, is on your heart and we have no way of removing it unless we take your heart out, but it a 5% chance you will live after words." He explain.

"I see." Twilight said.

She turn and look out the window, the face of her Changeling self took her real face. Celestia step up and ask, "What wrong Twilight?"

"I met the leader of the Space Ponies or I think she is." Twilight answer.

"She?" Pinkie ask.

"I'm not sure what she is, but she looks like a cross of a Changeling and myself. And her voice also has a cross of mine and Chrysalis's voice." Twilight explain the best she can.

"A Changeling that look like you and mix your and Chrysalis's voice?" Rainbow Dash ask to make sure.

"Yes and she hit me and the others with a strange magic beam. Then she pick me and 'thank' me for 'freeing' her. But I don't know where she came from or why she said that." Twilight said.

Celestia was in thought of what Twilight was saying. Then Twilight place her hoof over heart as if she was in pain.

"Twilight? Are you all right?" Celestia ask.

"I don't think so...AGHHHHHH!" Twilight stated to said but scream.

Deep inside of Twilight and at her heart. A blue gob, that had vines like around it, has finally connect itself to Twilight heart. It release a blue wave that fond it way to Twilight magic source and try to take over it but was to weak. It did however had a affect on Twilight.

Back with Twilight, She lower herself to the ground and grab her heard near her horn. Then blue lines crack down her horn and on to her body. They move in different directions, going up, down, left, right and other ways. Some of the lines went to her eyes, down to her hooves and even to her Cutie Mark. Her eyes snap open to show a blue glow in them and her Cutie mark was blue and shine as well. Then her Mane and Tail move upwards and started to flicker as if they were on fire. Sure enough they did turn in fire, but instead if the red fire they all knew, this one was blue.

The new look and power continue to stay and so did Twilight's screams. The rest of the Mane 6 whated to rush up to her but Celestia stop them.

"DON'T GO NEAR HER!" She shouted.

They back off and Celestia spoke to Twilight.

"Twilight! Whatever happen, fight it! Show you can handle it! Like how I help you control your magic!" She said.

The words got through and Twilight use her magic to open the window and jump out. Celestia follow with a teleport spell and saw Twilight standing to some boulders.

"Grrr..." Twilight said as she try to call whatever power she had to her horn. Finally a blue glow appear on Twilight's horn.

"Grrr...AHHHHHH!" Twilight shouted and fire a power beam that destroy the boulders in one shot. That all it took, once the beam fade so did the blue flames, lines, and glows. Twilight fell on the ground wake but weaken a little.

"What was that?" Rainbow ask.

"I'm guessing that it a new kind of Magic." Rarity said.

"It also the same type as the Space Ponies use on me and the others." Twilight said.

"Let's get you back inside. I think it best for you to stay for a while." Doctor Stable said.

Twilight nods and stand ups.

"By the way Twilight, the doctors says that you been asleep form a month!" Pinkie said hopping next to her.

Twilight fell over and didn't get back up. Celestia use her magic to pick her up.

"You has us all worry, my student. And we all glad to see you are well." She said showing that the past month wasn't the same.

As Twilight started to fall after Celestia was done talking one more thought enter her mind.

_'Charge Beam ability active. Can now store magic to release stronger attacks. Also can spin in the air to hit emeries.'_

Twilight couldn't think on what it means because she pass out as soon as the thought finish. Twilight slept a dreamless sleep as she was carry back to the Hospital.

* * *

And Stopping here. I have others Stories to work on but I need a break. This will continue but later. Please review.


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